ir.pl.clonotype_network(
adata_cohort_1_aa, color="patient_id", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'Patient_clonotype' as categorical /home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'expansion_on' as categorical /home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'E2F4_activity' as categorical
<matplotlib.axes._subplots.AxesSubplot at 0x7f01511b45b0>
ir.pl.clonotype_network(
adata_cohort_1_aa, color="timepoint", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01510e07f0>
ir.pl.clonotype_network(
adata_cohort_1_aa, color="cell_type", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01510b4820>
ir.pl.clonotype_network(
adata_cohort_1_aa, color="expansion_on", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0197f82820>
ir.pl.clonotype_network(
adata_cohort_1_aa, color="expansion", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01fd656910>
# VDJDB antigen annotation
ir.pl.clonotype_network(
adata_cohort_1_aa, color="VDJdb", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f016d97a2b0>
# IEDB antigen annotation
ir.pl.clonotype_network(
adata_cohort_1_aa, color="IEDB", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01f73d2a60>
ir.pl.clonotype_network(
adata_cohort_1_aa, color="E2F4_score", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01f73d2910>
ir.pl.clonotype_network(
adata_cohort_1_aa, color="E2F4_activity", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01f80a6c10>
ir.pl.clonotype_network(
adata_cohort_2_aa, color="patient_id", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'Patient_clonotype' as categorical /home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'expansion_on' as categorical
<matplotlib.axes._subplots.AxesSubplot at 0x7f0104af87c0>
ir.pl.clonotype_network(
adata_cohort_2_aa, color="timepoint", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f013934f970>
ir.pl.clonotype_network(
adata_cohort_2_aa, color="cell_type", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0105c55ee0>
ir.pl.clonotype_network(
adata_cohort_2_aa, color="expansion_on", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f01f40fea00>
ir.pl.clonotype_network(
adata_cohort_2_aa, color="expansion", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0232b31250>
# VDJDB antigen annotation
ir.pl.clonotype_network(
adata_cohort_2_aa, color="VDJdb", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0236017700>
# IEDB antigen annotation
ir.pl.clonotype_network(
adata_cohort_2_aa, color="IEDB", base_size=10, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0236d71160>
ir.pl.clonotype_network(
adata_aa, color="patient_id", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
/home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'Patient_clonotype' as categorical /home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'expansion_on' as categorical /home/ausserh/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1220: FutureWarning: The `inplace` parameter in pandas.Categorical.reorder_categories is deprecated and will be removed in a future version. Removing unused categories will always return a new Categorical object. c.reorder_categories(natsorted(c.categories), inplace=True) ... storing 'E2F4_activity' as categorical
<matplotlib.axes._subplots.AxesSubplot at 0x7f08c42bc670>
ir.pl.clonotype_network(
adata_aa, color="timepoint", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f09090f77f0>
ir.pl.clonotype_network(
adata_aa, color="response", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0908fbf400>
ir.pl.clonotype_network(
adata_aa, color="cell_type", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f0908fb7ee0>
ir.pl.clonotype_network(
adata_aa, color="expansion_on", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f08c26548e0>
ir.pl.clonotype_network(
adata_aa, color="VDJdb", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f08adfaabb0>
ir.pl.clonotype_network(
adata_aa, color="IEDB", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f091ecc8ca0>
ir.pl.clonotype_network(
adata_aa, color="E2F4_score", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f091db90700>
ir.pl.clonotype_network(
adata_aa, color="E2F4_activity", base_size=3, label_fontsize=9, panel_size=(7, 7)
)
<matplotlib.axes._subplots.AxesSubplot at 0x7f091de60d00>